Summary: Long-chain fatty aldehyde decarbonylase
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Long-chain fatty aldehyde decarbonylase Provide feedback
This cyanobacterial family of fatty aldehyde decarbonylases acts on mainly C16 and C18 substrates to form hydrocarbons and carbon monoxide [1]. Note that the corresponding EC number ( EC:4.1.99.5) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase.
Literature references
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Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB;, Science. 2010;329:559-562.: Microbial biosynthesis of alkanes. PUBMED:20671186 EPMC:20671186
Internal database links
SCOOP: | AurF DUF455 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR022612
This cyanobacterial family of fatty aldehyde decarbonylases acts on mainly C16 and C18 substrates to form hydrocarbons and carbon monoxide [PUBMED:20671186]. Note that the corresponding EC number (EC) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | aldehyde decarbonylase activity (GO:0071771) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan Ferritin (CL0044), which has the following description:
The members of this clan all share a distinctive four helical bundle. The four helices are arranged antiparallel with a left-handed twist. This helical bundle is distinguished from others by the long connection between the second and third helices. Some of the members contain a Fe or Mn dimer at the centre of the helical bundle. The ferritin fold was first described by Murzin AG and Chothia C, Cur Opin Struc Biol 1992, 2:895-903.
The clan contains the following 25 members:
Ald_deCOase AOX AurF Coat_F COQ7 DUF2202 DUF2383 DUF305 DUF3231 DUF4142 DUF4439 DUF455 DUF5623 DUF892 FA_desaturase_2 Ferritin Ferritin-like Ferritin_2 MiaE MiaE_2 Mn_catalase PaaA_PaaC Phenol_Hydrox Ribonuc_red_sm RubrerythrinAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (21) |
Full (167) |
Representative proteomes | UniProt (654) |
NCBI (1035) |
Meta (296) |
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RP15 (7) |
RP35 (73) |
RP55 (160) |
RP75 (293) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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not generated,
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (21) |
Full (167) |
Representative proteomes | UniProt (654) |
NCBI (1035) |
Meta (296) |
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RP15 (7) |
RP35 (73) |
RP55 (160) |
RP75 (293) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_3735 (release 23.0) |
Previous IDs: | DUF3066; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Pollington J |
Number in seed: | 21 |
Number in full: | 167 |
Average length of the domain: | 213.10 aa |
Average identity of full alignment: | 55 % |
Average coverage of the sequence by the domain: | 85.00 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 218 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
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Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ald_deCOase domain has been found. There are 29 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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